GEX_phenotype_per_clone: Plotting of GEX phenotype by VDJ clone

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Plotting of GEX phenotype by VDJ clone

Description

Integrates VDJ and gene expression libraries by providing cluster membership seq_per_vdj object and the index of the cell in the Seurat RNA-seq object. ! For platypus.version == "v3" and VDJ_GEX_matrix output the function will iterate over entries in the sample_id column of the GEX by default.

Usage

GEX_phenotype_per_clone(
  GEX,
  clonotype.ids,
  global.clonotypes,
  GEX.group.by,
  GEX.clonotypes,
  platypus.version
)

Arguments

GEX	For platypus.version == "v3" the GEX object from the output of the VDJ_GEX_matrix function (VDJ_GEX_matrix.output \[\[2\]\]). For platypus.version == "v2" a single seurat object from automate_GEX function after labeling cell phenotypes using the GEX_phenotype function.
clonotype.ids	For platypus.version == "v2" Output from either VDJ_analyze or VDJ_clonotype functions. This list should correspond to a single GEX.list object, in which each list element in clonotype.list is found in the GEX.object. Furthermore, these repertoires should be found in the automate_GEX library.
global.clonotypes	Boolean. Defaults to FALSE. Set to True if clonotyping has been done across samples
GEX.group.by	For platypus.version == "v3". Character. Column name of the [e-mail] to group barplot by. Defaults to seurat_clusters
GEX.clonotypes	For platypus.version == "v3". Numeric vector with ids of clonotypes to plot e.g. c(1,2,3,4). Can also be set to "topclones"
platypus.version	Set to either "v2" or "v3" depending on wether suppyling GEX_automate or VDJ_GEX_matrix\[\[2\]\] objects. Defaults to "v3"

Value

Returns a stacked barplot that visualizes the seurat cluster membership for different cell phenotypes.

Examples

small_vgm_cl <- Platypus::small_vgm
small_vgm_cl[[2]]$clonotype_id_10x <- "clonotype1"
GEX_phenotype_per_clone(GEX = small_vgm_cl[[2]]
, GEX.clonotypes = c(1), GEX.group.by = "seurat_clusters", platypus.version = "v3")

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.